cDNAs encoding for neuropeptide Y (NPY), cocaine and amphetamine regulated transcript (CART) and cholecystokinin (CCK) were cloned in winter flounder, a species that undergoes a period of natural fasting during the winter. Tissue distribution studies show that these peptides are present in several peripheral tissues, including gut and gonads, as well as within the brain. We assessed the effects of season and fasting on the expression of these peptides. Our results show that NPY and CCK, but not CART, show seasonal differences in expression with higher hypothalamic NPY and lower gut CCK expression levels in the winter. In the summer, fasting induced an increase in hypothalamic NPY expression levels and a decrease in gut CCK levels, but did not affect hypothalamic CART expression levels. None of the peptides examined was affected by fasting in the winter. Our results suggest that NPY and CCK, but maybe not CART, might have a major role in the regulation of feeding in winter flounder and might contribute to the seasonal fluctuations in appetite in this species.